In short: an underactive thyroid (hypothyroidism) is one of the better-documented risk factors for SIBO. In a 2007 study of people with Hashimoto’s thyroiditis, 54% had SIBO compared with 5% of controls¹, and a 2026 records study found that hypothyroidism roughly doubled the 10-year risk of a SIBO diagnosis². The most likely reason is that low thyroid hormone slows the gut. In that study, the extra risk appeared lower in people taking levothyroxine², but SIBO and other gut problems can make levothyroxine tablets harder to absorb⁴.

Why the thyroid matters for the gut

Thyroid hormone affects how fast the digestive tract moves. When levels are low, the gut slows, and slow movement of the small intestine is one of the main causes of SIBO because it weakens the migrating motor complex that sweeps bacteria out¹. The 2007 study’s authors also proposed that excess bacteria could interfere with how levothyroxine is absorbed¹.

Hashimoto’s thyroiditis (also called autoimmune thyroiditis) is a common cause of hypothyroidism. It is an autoimmune disease in which the immune system gradually damages the thyroid.

What the studies show

Study	Who was studied	Result
2007, Italy	50 people with a history of overt hypothyroidism from Hashimoto's, and 40 controls; glucose breath test	SIBO in 54% vs. 5%¹
2017, Germany	Records of 1,809 people who had a breath test for gut symptoms	Hypothyroidism (odds ratio 2.6) and levothyroxine use (3.0) were both linked to SIBO; levothyroxine was the strongest single predictor in a simplified model³
2026, USA	Small-intestinal fluid from 49 people with hypothyroidism and 323 controls, plus a health-records analysis	SIBO in 33% vs. 15% by culture. In the records, 10-year risk was 2.2 times higher with hypothyroidism and 2.4 times higher with autoimmune thyroiditis²
2021, China	224 pregnant women with subclinical hypothyroidism and 196 with normal thyroid function; lactulose breath test	SIBO in 56.7% vs. 31.6%⁵
2022, China	231 pregnant women with hypothyroidism and 210 without; lactulose breath test	SIBO in 48.5% vs. 24.8%⁶

In the 2007 study, bloating, flatulence and abdominal discomfort were more common in those with SIBO, and they improved after a week of the antibiotic rifaximin. Clearing SIBO did not change thyroid hormone levels¹. The 2026 study also found differences in the bacteria of the small intestine: in people with hypothyroidism and SIBO, Klebsiella species were common².

Does levothyroxine raise or lower the risk?

The studies point in different directions. In the 2026 records analysis, the extra SIBO risk appeared to be much lower in people taking levothyroxine². In the 2017 records study, levothyroxine use was itself one of the strongest predictors of SIBO³.

These findings are not necessarily contradictory. Levothyroxine use also marks people who have thyroid disease, and a dose that does not fully correct thyroid levels would leave the gut slow. Both studies are based on records and cannot show cause and effect. We found no evidence that levothyroxine itself causes SIBO.

SIBO and thyroid tablet absorption

Levothyroxine is often poorly absorbed in people with gut conditions⁴. In a 2024 open-label study of 75 people with hypothyroidism and IBS, 65% had SIBO. When they switched from tablets to liquid levothyroxine at the same dose, more people reached a normal TSH (78% vs. 57% on tablets), and both thyroid and IBS symptoms improved⁴. The study had no control group, and it was partly funded by IBSA, a company that makes liquid levothyroxine⁴.

If your thyroid levels are hard to keep in range despite taking your tablets correctly, ask your doctor whether a gut problem such as SIBO could be affecting absorption.

Treatment

SIBO linked to hypothyroidism is treated like other SIBO; see our treatment overview and antibiotics guide. In the 2007 study, rifaximin 1,200 mg a day for a week improved gut symptoms¹.

Two Chinese studies in pregnant women with hypothyroidism and SIBO tested 21 days of probiotics with prebiotics alongside levothyroxine. Breath test gas levels, constipation and some blood markers improved after treatment, but neither study had an untreated comparison group⁶⁷. Both, like the 2021 pregnancy study, come from the same research group, so they are not independent confirmations. See probiotics for SIBO.

Because slow gut movement is the likely link, getting thyroid levels into range is the step most likely to help prevent SIBO from returning; see preventing SIBO relapse.

Common questions

Can SIBO cause Hashimoto’s?

We found no evidence that it does. The studies show that SIBO is more common in people who already have hypothyroidism or Hashimoto’s¹², which fits with low thyroid hormone slowing the gut.

Will treating SIBO improve my thyroid levels?

In the 2007 study, clearing SIBO improved gut symptoms but did not change thyroid hormone levels¹. It may help if SIBO is interfering with tablet absorption, but that has not been tested directly.

Should people with hypothyroidism be tested for SIBO?

We found no guideline that recommends testing everyone with hypothyroidism. Testing makes sense if you have bloating, gas, diarrhea or other SIBO symptoms, or if your thyroid levels are unexpectedly hard to control. See breath tests explained.

Works Cited & Scientific References 7

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SIBO and Hypothyroidism: Hashimoto's, Levothyroxine and Gut Motility